Hi there,
I am testing acpypi/antechamber in a pipeline over ~9000 ligands.
And then I bumped in this case (file attached):
Ium.none_neutral.pdb.mol2
It contains an Uranium atom (U) and then sqm should failed (as it does on my
Mac), from sqm.out:
--------------------------------------------------------------------------------
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 7
QMMM: Atom number: 3 has atomic number 92.
QMMM: There are no AM1 parameters for this element. Sorry.
SANDER BOMB in subroutine qm2_load_params
UNSUPPORTED ELEMENT
QM AM1 NOT AVAILABLE FOR THIS ATOM
But, for my surprise, on Linux (AT 1.3 with gcc, 64 bits)
--------------------------------------------------------------------------------
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 6
[snip]
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 O -18.5780 27.2260 13.4290
QMMM: 2 2 O -17.7590 27.9890 16.9560
QMMM: 3 3 -18.1050 27.7320 15.1890
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
QMMM: WARNING!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: Job will continue with unconverged SCF. Warning energies
QMMM: and forces for this step will not be accurate.
QMMM: E = -0.6277E+05 DeltaE = -0.6792E-07 DeltaP = 0.5814E-09
QMMM: Smallest DeltaE = 0.5187E-07 DeltaP = 0.6411E-09 Step = 999
sqm energy: 10 -47006.6679 181.335107
sqm energy: 20 -47004.5249 181.291974
sqm energy: 30 -47002.3674 181.252312
sqm energy: 40 -47000.1955 181.216010
sqm energy: 50 -46998.0094 181.182955
[snip]
sqm energy: 9990 -46022.7694 177.831885
Final SCF energy is -46022.769139155607
Atomic Charges for Step 1 :
Atom Element Mulliken Charge
1 O 1.184287
2 O 4.815713
3 -6.000000
Total Mulliken Charge = -0.000000
Final Structure
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 O -19.1849 26.8630 14.7333
QMMM: 2 2 O -17.1643 28.4815 15.5279
QMMM: 3 3 -18.0929 27.6025 15.3128
--------- Calculation Completed ----------
And the sqm.in in both machines is the SAME:
Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0002,
tight_p_conv=1, scfconv=1.d-10, qmcharge=0,
/
8 O1 -18.5780 27.2260 13.4290
8 O2 -17.7590 27.9890 16.9560
92 U -18.1050 27.7320 15.1890
Many thanks in advance,
Alan
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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Received on Thu Jan 14 2010 - 04:30:02 PST
